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Conserved domains on  [gi|569006445|ref|XP_006526763|]
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lymphocyte-specific helicase isoform X2 [Mus musculus]

Protein Classification

DEAD/DEAH box helicase( domain architecture ID 1000678)

DEAD/DEAH box containing ATP-dependent helicase, similar to ISWI chromatin-remodeling complex ATPases, which are catalytic components of ISW1-type complexes, which act by remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03142 super family cl33647
Probable chromatin-remodeling complex ATPase chain; Provisional
 4-437 6.82e-108

Probable chromatin-remodeling complex ATPase chain; Provisional


The actual alignment was detected with superfamily member PLN03142:

Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 343.32  E-value: 6.82e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445    4 RLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDITSlsetaediiaKEREQNVLHMLHQIL 83
Cdd:PLN03142  309 LLSKTMRLFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISG----------ENDQQEVVQQLHKVL 378

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   84 TPFLLRRLKSDVALEVPPKREVVVYAPLCNKQEIFYTAIvnrtianmfgsceketvelsptgrpkrrsrksinyseldqf 163
Cdd:PLN03142  379 RPFLLRRLKSDVEKGLPPKKETILKVGMSQMQKQYYKAL----------------------------------------- 417

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  164 pseLEKLISQIQPEVNRERtvvegnipiesevnlkLRNIMMLLRKCCNHPYMIE--YPIDPvtqeFKIDEELVTNSGKFL 241
Cdd:PLN03142  418 ---LQKDLDVVNAGGERKR----------------LLNIAMQLRKCCNHPYLFQgaEPGPP----YTTGEHLVENSGKMV 474

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  242 ILDRMLPELKKRGHKVLVFSQMTSMLDILMDYCHLRNFIFSRLDGSMSYSEREKNIYSFNTD-PDVFLFLVSTRAGGLGI 320
Cdd:PLN03142  475 LLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPgSEKFVFLLSTRAGGLGI 554

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  321 NLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPVVVYRLVTANTIDQKIVERAAAKRKLEKLIIHknhfkggQSGLSQ 400
Cdd:PLN03142  555 NLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVIQ-------QGRLAE 627

                         410       420       430
                  ....*....|....*....|....*....|....*...
gi 569006445  401 SKNfLDAKELMELLKsrdYERE-VKGSREKVISDEDLE 437
Cdd:PLN03142  628 QKT-VNKDELLQMVR---YGAEmVFSSKDSTITDEDID 661
 
Name Accession Description Interval E-value
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
 4-437 6.82e-108

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 343.32  E-value: 6.82e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445    4 RLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDITSlsetaediiaKEREQNVLHMLHQIL 83
Cdd:PLN03142  309 LLSKTMRLFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISG----------ENDQQEVVQQLHKVL 378

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   84 TPFLLRRLKSDVALEVPPKREVVVYAPLCNKQEIFYTAIvnrtianmfgsceketvelsptgrpkrrsrksinyseldqf 163
Cdd:PLN03142  379 RPFLLRRLKSDVEKGLPPKKETILKVGMSQMQKQYYKAL----------------------------------------- 417

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  164 pseLEKLISQIQPEVNRERtvvegnipiesevnlkLRNIMMLLRKCCNHPYMIE--YPIDPvtqeFKIDEELVTNSGKFL 241
Cdd:PLN03142  418 ---LQKDLDVVNAGGERKR----------------LLNIAMQLRKCCNHPYLFQgaEPGPP----YTTGEHLVENSGKMV 474

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  242 ILDRMLPELKKRGHKVLVFSQMTSMLDILMDYCHLRNFIFSRLDGSMSYSEREKNIYSFNTD-PDVFLFLVSTRAGGLGI 320
Cdd:PLN03142  475 LLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPgSEKFVFLLSTRAGGLGI 554

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  321 NLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPVVVYRLVTANTIDQKIVERAAAKRKLEKLIIHknhfkggQSGLSQ 400
Cdd:PLN03142  555 NLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVIQ-------QGRLAE 627

                         410       420       430
                  ....*....|....*....|....*....|....*...
gi 569006445  401 SKNfLDAKELMELLKsrdYERE-VKGSREKVISDEDLE 437
Cdd:PLN03142  628 QKT-VNKDELLQMVR---YGAEmVFSSKDSTITDEDID 661
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 4-386 1.64e-89

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 287.12  E-value: 1.64e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   4 RLIRELKrfnADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFditslsetaEDIIAKEREQNvLHMLHQIL 83
Cdd:COG0553  379 KAVRALK---ARHRLALTGTPVENRLEELWSLLDFLNPGLLGSLKAFRERF---------ARPIEKGDEEA-LERLRRLL 445

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  84 TPFLLRRLKSDVALEVPPKREVVVYAPLCNKQEIFYTAIVNRTIANMfgsceketvelspTGRPKRRSRKSInyseldqf 163
Cdd:COG0553  446 RPFLLRRTKEDVLKDLPEKTEETLYVELTPEQRALYEAVLEYLRREL-------------EGAEGIRRRGLI-------- 504

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445 164 pseleklisqiqpevnrertvvegnipiesevnLKLrniMMLLRKCCNHPYMIeypidpvtqeFKIDEELVTNSGKFLIL 243
Cdd:COG0553  505 ---------------------------------LAA---LTRLRQICSHPALL----------LEEGAELSGRSAKLEAL 538

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445 244 DRMLPELKKRGHKVLVFSQMTSMLDILMDYCHLRNFIFSRLDGSMSYSEREKNIYSFNTDPDVFLFLVSTRAGGLGINLT 323
Cdd:COG0553  539 LELLEELLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQEGPEAPVFLISLKAGGEGLNLT 618

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 569006445 324 AADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPVVVYRLVTANTIDQKIVERAAAKRKLEKLII 386
Cdd:COG0553  619 AADHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEEKILELLEEKRALAESVL 681
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 237-362 7.80e-65

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 205.40  E-value: 7.80e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445 237 SGKFLILDRMLPELKKRGHKVLVFSQMTSMLDILMDYCHLRNFIFSRLDGSMSYSEREKNIYSFNTDPDVFLFLVSTRAG 316
Cdd:cd18793   10 SGKLEALLELLEELREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPDIRVFLLSTKAG 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 569006445 317 GLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPVVVYRLV 362
Cdd:cd18793   90 GVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQKKPVVVYRLI 135
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 2-216 2.74e-37

SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.


Pssm-ID: 425504 [Multi-domain]  Cd Length: 289  Bit Score: 138.20  E-value: 2.74e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445    2 KCRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDITSLSETAEDIIAKereqnvlhmLHQ 81
Cdd:pfam00176 139 KSKLSKALKSLKTRNRWILTGTPLQNNLEELWALLNFLRPGPFGSLSTFRNWFDRPIERGGGKKGVSR---------LHK 209

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   82 ILTPFLLRRLKSDVALEVPPKREVVVYAPLCNKQEIFYTAIVnrtianmfgsceketvelsptgrpkrrsrksinyseld 161
Cdd:pfam00176 210 LLKPFLLRRTKKDVEKSLPPKVEYILFCRLSKLQRKLYQTFL-------------------------------------- 251

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 569006445  162 qfpseLEKLISQIQpevnrertvvegNIPIESEVNLKLRNIMMLLRKCCNHPYMI 216
Cdd:pfam00176 252 -----LKKDLNAIK------------TGEGGREIKASLLNILMRLRKICNHPGLI 289
HELICc smart00490
helicase superfamily c-terminal domain;
268-351 7.47e-23

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 91.89  E-value: 7.47e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   268 DILMDYCHLRNFIFSRLDGSMSYSEREKNIYSFNTDPDVFLflVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRC 347
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVL--VATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78


                   ....
gi 569006445   348 HRIG 351
Cdd:smart00490  79 GRAG 82
DISARM_DrmD_b NF038318
DISARM system SNF2-like helicase DrmD, short form; DrmD, a SNF2-like helicase, is a component ...
 17-381 3.71e-10

DISARM system SNF2-like helicase DrmD, short form; DrmD, a SNF2-like helicase, is a component of class 1 DISARM (Defence Island System Associated with Restriction Modification), which contains a DNA adenine N6 methyltransferase. This HMM describes a distinct form that is somewhat shorter than the majority of DrmD proteins.


Pssm-ID: 468472 [Multi-domain]  Cd Length: 868  Bit Score: 62.39  E-value: 3.71e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  17 KLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFdITSlsetaEDIIAKEREqnvlhmlhqiLTPFLLRRLKSDVA 96
Cdd:NF038318 183 KILLTATPLQNSLLDLYGLVSFIDPRIFGSEKVFSKRY-IKD-----EDYSDLKRE----------LSPVLYRTLRKDVA 246

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  97 --------------LEVPPKrEVVVYAPLCN--KQEIFYtAI--VNRT-----IANMFGSCE---KETVELSptgrpKRR 150
Cdd:NF038318 247 dymqfkkrkcitvdFELSPD-EIELYVRVNNflKRDILY-SIptSNRTliilvIRKLLASSSfalAETFEVL-----KKR 319

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445 151 ------SRKSINYSE-LDQFPSELEKLISQ-----------------IQPEVNRERTVVEGNIPIESevNLKLRNIMMLL 206
Cdd:NF038318 320 leklkeGTRSANAQEgFDLFWSFVEDEIDEsgfeekqdelytrqkefIQHEIDEVDAIIDVAKRIKT--NAKVTALKTAL 397

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445 207 RKCCNHpymieypidpvTQEFKIDEELVTNSGKFLILDRMLPELKKRGHK---VLVFSQMTS--MLDILMDYCHLRNF-- 279
Cdd:NF038318 398 EIAFEY-----------QREEGIAQKVVVFTESKRTQKYIAEELRKSGYEgedILLFNGDFDdaMTKEIYRAWQVKNYgk 466

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445 280 -IFSRldgSMSYsereKN--IYSFNTDPDVflfLVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPV 356
Cdd:NF038318 467 aNYGR---SVEY----KHaiVDYFKNNAKI---LIVTDAGSEGLNLQFCNTVINYDLPWNPQKIEQRIGRCHRYGQKNDV 536

                        410       420
                 ....*....|....*....|....*.
gi 569006445 357 VVYRLV-TANTIDQKIVERAAAKRKL 381
Cdd:NF038318 537 VAINLLnTQNVADKRVYEILSEKFEL 562
 
Name Accession Description Interval E-value
PLN03142 PLN03142
Probable chromatin-remodeling complex ATPase chain; Provisional
 4-437 6.82e-108

Probable chromatin-remodeling complex ATPase chain; Provisional


Pssm-ID: 215601 [Multi-domain]  Cd Length: 1033  Bit Score: 343.32  E-value: 6.82e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445    4 RLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDITSlsetaediiaKEREQNVLHMLHQIL 83
Cdd:PLN03142  309 LLSKTMRLFSTNYRLLITGTPLQNNLHELWALLNFLLPEIFSSAETFDEWFQISG----------ENDQQEVVQQLHKVL 378

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   84 TPFLLRRLKSDVALEVPPKREVVVYAPLCNKQEIFYTAIvnrtianmfgsceketvelsptgrpkrrsrksinyseldqf 163
Cdd:PLN03142  379 RPFLLRRLKSDVEKGLPPKKETILKVGMSQMQKQYYKAL----------------------------------------- 417

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  164 pseLEKLISQIQPEVNRERtvvegnipiesevnlkLRNIMMLLRKCCNHPYMIE--YPIDPvtqeFKIDEELVTNSGKFL 241
Cdd:PLN03142  418 ---LQKDLDVVNAGGERKR----------------LLNIAMQLRKCCNHPYLFQgaEPGPP----YTTGEHLVENSGKMV 474

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  242 ILDRMLPELKKRGHKVLVFSQMTSMLDILMDYCHLRNFIFSRLDGSMSYSEREKNIYSFNTD-PDVFLFLVSTRAGGLGI 320
Cdd:PLN03142  475 LLDKLLPKLKERDSRVLIFSQMTRLLDILEDYLMYRGYQYCRIDGNTGGEDRDASIDAFNKPgSEKFVFLLSTRAGGLGI 554

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  321 NLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPVVVYRLVTANTIDQKIVERAAAKRKLEKLIIHknhfkggQSGLSQ 400
Cdd:PLN03142  555 NLATADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKKLALDALVIQ-------QGRLAE 627

                         410       420       430
                  ....*....|....*....|....*....|....*...
gi 569006445  401 SKNfLDAKELMELLKsrdYERE-VKGSREKVISDEDLE 437
Cdd:PLN03142  628 QKT-VNKDELLQMVR---YGAEmVFSSKDSTITDEDID 661
HepA COG0553
Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, ...
 4-386 1.64e-89

Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair];


Pssm-ID: 440319 [Multi-domain]  Cd Length: 682  Bit Score: 287.12  E-value: 1.64e-89
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   4 RLIRELKrfnADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFditslsetaEDIIAKEREQNvLHMLHQIL 83
Cdd:COG0553  379 KAVRALK---ARHRLALTGTPVENRLEELWSLLDFLNPGLLGSLKAFRERF---------ARPIEKGDEEA-LERLRRLL 445

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  84 TPFLLRRLKSDVALEVPPKREVVVYAPLCNKQEIFYTAIVNRTIANMfgsceketvelspTGRPKRRSRKSInyseldqf 163
Cdd:COG0553  446 RPFLLRRTKEDVLKDLPEKTEETLYVELTPEQRALYEAVLEYLRREL-------------EGAEGIRRRGLI-------- 504

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445 164 pseleklisqiqpevnrertvvegnipiesevnLKLrniMMLLRKCCNHPYMIeypidpvtqeFKIDEELVTNSGKFLIL 243
Cdd:COG0553  505 ---------------------------------LAA---LTRLRQICSHPALL----------LEEGAELSGRSAKLEAL 538

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445 244 DRMLPELKKRGHKVLVFSQMTSMLDILMDYCHLRNFIFSRLDGSMSYSEREKNIYSFNTDPDVFLFLVSTRAGGLGINLT 323
Cdd:COG0553  539 LELLEELLAEGEKVLVFSQFTDTLDLLEERLEERGIEYAYLHGGTSAEERDELVDRFQEGPEAPVFLISLKAGGEGLNLT 618

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 569006445 324 AADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPVVVYRLVTANTIDQKIVERAAAKRKLEKLII 386
Cdd:COG0553  619 AADHVIHYDLWWNPAVEEQAIDRAHRIGQTRDVQVYKLVAEGTIEEKILELLEEKRALAESVL 681
SF2_C_SNF cd18793
C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) ...
 237-362 7.80e-65

C-terminal helicase domain of the SNF family helicases; The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350180 [Multi-domain]  Cd Length: 135  Bit Score: 205.40  E-value: 7.80e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445 237 SGKFLILDRMLPELKKRGHKVLVFSQMTSMLDILMDYCHLRNFIFSRLDGSMSYSEREKNIYSFNTDPDVFLFLVSTRAG 316
Cdd:cd18793   10 SGKLEALLELLEELREPGEKVLIFSQFTDTLDILEEALRERGIKYLRLDGSTSSKERQKLVDRFNEDPDIRVFLLSTKAG 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 569006445 317 GLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPVVVYRLV 362
Cdd:cd18793   90 GVGLNLTAANRVILYDPWWNPAVEEQAIDRAHRIGQKKPVVVYRLI 135
DEXHc_HELLS_SMARCA6 cd18009
DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or ...
 1-92 1.36e-56

DEXH-box helicase domain of HELLS; HELLS (helicase, lymphoid specific, also known as Lsh or SMARCA6) is a major epigenetic regulator crucial for normal heterochromatin structure and function. HELLS is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350767 [Multi-domain]  Cd Length: 236  Bit Score: 187.59  E-value: 1.36e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   1 MKCRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDITSLSETAEDI--IAKEREQNVLHM 78
Cdd:cd18009  143 LNCRLIQELKTFNSDNRLLLTGTPLQNNLSELWSLLNFLLPDVFDDLSSFESWFDFSSLSDNAADIsnLSEEREQNIVHM 222

                         90
                 ....*....|....
gi 569006445  79 LHQILTPFLLRRLK 92
Cdd:cd18009  223 LHAILKPFLLRRLK 236
SNF2-rel_dom pfam00176
SNF2-related domain; This domain is found in proteins involved in a variety of processes ...
 2-216 2.74e-37

SNF2-related domain; This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.


Pssm-ID: 425504 [Multi-domain]  Cd Length: 289  Bit Score: 138.20  E-value: 2.74e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445    2 KCRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDITSLSETAEDIIAKereqnvlhmLHQ 81
Cdd:pfam00176 139 KSKLSKALKSLKTRNRWILTGTPLQNNLEELWALLNFLRPGPFGSLSTFRNWFDRPIERGGGKKGVSR---------LHK 209

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   82 ILTPFLLRRLKSDVALEVPPKREVVVYAPLCNKQEIFYTAIVnrtianmfgsceketvelsptgrpkrrsrksinyseld 161
Cdd:pfam00176 210 LLKPFLLRRTKKDVEKSLPPKVEYILFCRLSKLQRKLYQTFL-------------------------------------- 251

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 569006445  162 qfpseLEKLISQIQpevnrertvvegNIPIESEVNLKLRNIMMLLRKCCNHPYMI 216
Cdd:pfam00176 252 -----LKKDLNAIK------------TGEGGREIKASLLNILMRLRKICNHPGLI 289
Helicase_C pfam00271
Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, ...
 238-351 1.30e-29

Helicase conserved C-terminal domain; The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.


Pssm-ID: 459740 [Multi-domain]  Cd Length: 109  Bit Score: 111.53  E-value: 1.30e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  238 GKFLILDRMLPelKKRGHKVLVFSQMTSMLDILMdYCHLRNFIFSRLDGSMSYSEREKNIYSFNTDPdvFLFLVSTRAGG 317
Cdd:pfam00271   1 EKLEALLELLK--KERGGKVLIFSQTKKTLEAEL-LLEKEGIKVARLHGDLSQEEREEILEDFRKGK--IDVLVATDVAE 75

                          90       100       110
                  ....*....|....*....|....*....|....
gi 569006445  318 LGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIG 351
Cdd:pfam00271  76 RGLDLPDVDLVINYDLPWNPASYIQRIGRAGRAG 109
DEXHc_SMARCA2_SMARCA4 cd17996
DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin ...
 1-92 5.03e-29

DEXH-box helicase domain of SMARCA2 and SMARCA4; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, members 2 and 4 (SMARCA2 and SMARCA4) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350754 [Multi-domain]  Cd Length: 233  Bit Score: 114.00  E-value: 5.03e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   1 MK---CRLIRELKR-FNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDITSLSETAEDIIAKEREQNVL 76
Cdd:cd17996  136 MKnaqSKLTQTLNTyYHARYRLLLTGTPLQNNLPELWALLNFLLPKIFKSCKTFEQWFNTPFANTGEQVKIELNEEETLL 215

                         90
                 ....*....|....*...
gi 569006445  77 --HMLHQILTPFLLRRLK 92
Cdd:cd17996  216 iiRRLHKVLRPFLLRRLK 233
DEXHc_SMARCA1_SMARCA5 cd17997
DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin ...
 9-92 1.19e-27

DEAH-box helicase domain of SMARCA1 and SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 and 5 (SMARCA1 and SMARCA5) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350755 [Multi-domain]  Cd Length: 222  Bit Score: 110.10  E-value: 1.19e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   9 LKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDITSLSETAEDIIAKereqnvlhmLHQILTPFLL 88
Cdd:cd17997  148 VRLFNSRNRLLLTGTPLQNNLHELWALLNFLLPDVFTSSEDFDEWFNVNNCDDDNQEVVQR---------LHKVLRPFLL 218


                 ....
gi 569006445  89 RRLK 92
Cdd:cd17997  219 RRIK 222
DEXHc_SMARCA5 cd18064
DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent ...
 2-103 8.93e-25

DEAH-box helicase domain of SMARCA5; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 (SMARCA5, also called SNF2H) is the catalytic subunit of the four known chromatin-remodeling complexes: CHRAC, RSF, ACF/WCRF, and WICH. SMARCA5 plays a major role organising arrays of nucleosomes adjacent to the binding sites for the architectural transcription factor CTCF sites and acts to promote CTCF binding SMARCA5 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350822 [Multi-domain]  Cd Length: 244  Bit Score: 102.44  E-value: 8.93e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   2 KCRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDITSLSEtaediiakerEQNVLHMLHQ 81
Cdd:cd18064  153 KSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALLNFLLPDVFNSAEDFDSWFDTNNCLG----------DQKLVERLHM 222

                         90       100
                 ....*....|....*....|..
gi 569006445  82 ILTPFLLRRLKSDVALEVPPKR 103
Cdd:cd18064  223 VLRPFLLRRIKADVEKSLPPKK 244
HELICc smart00490
helicase superfamily c-terminal domain;
268-351 7.47e-23

helicase superfamily c-terminal domain;


Pssm-ID: 197757 [Multi-domain]  Cd Length: 82  Bit Score: 91.89  E-value: 7.47e-23
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   268 DILMDYCHLRNFIFSRLDGSMSYSEREKNIYSFNTDPDVFLflVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRC 347
Cdd:smart00490   1 EELAELLKELGIKVARLHGGLSQEEREEILDKFNNGKIKVL--VATDVAERGLDLPGVDLVIIYDLPWSPASYIQRIGRA 78


                   ....
gi 569006445   348 HRIG 351
Cdd:smart00490  79 GRAG 82
DEXQc_SRCAP cd18003
DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or ...
 12-90 2.43e-22

DEXH/Q-box helicase domain of SRCAP; Snf2-related CBP activator (SRCAP, also known as SWR1 or DOMO1) is the core catalytic component of the multiprotein chromatin-remodeling SRCAP complex, that is necessary for the incorporation of the histone variant H2A.Z into nucleosomes. SRCAP is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350761 [Multi-domain]  Cd Length: 223  Bit Score: 95.11  E-value: 2.43e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  12 FNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFD--ITSLSETAEDIiakerEQNVLHMLHQILTPFLLR 89
Cdd:cd18003  148 FNTQRRLLLTGTPLQNSLMELWSLMHFLMPHIFQSHQEFKEWFSnpLTAMSEGSQEE-----NEELVRRLHKVLRPFLLR 222


                 .
gi 569006445  90 R 90
Cdd:cd18003  223 R 223
DEXHc_SMARCA1 cd18065
DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent ...
 2-92 2.68e-20

DEAH-box helicase domain of SMARCA1; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 (SMARCA1, also called SNF2L) is a component of NURF (nucleosome-remodeling factor) and CERF (CECR2-containing-remodeling factor) complexes which promote the perturbation of chromatin structure in an ATP-dependent manner. SMARCA1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350823 [Multi-domain]  Cd Length: 233  Bit Score: 89.69  E-value: 2.68e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   2 KCRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDITSLSEtaediiakerEQNVLHMLHQ 81
Cdd:cd18065  153 KSKLSEIVREFKTTNRLLLTGTPLQNNLHELWALLNFLLPDVFNSADDFDSWFDTKNCLG----------DQKLVERLHA 222

                         90
                 ....*....|.
gi 569006445  82 ILTPFLLRRLK 92
Cdd:cd18065  223 VLKPFLLRRIK 233
DEXQc_INO80 cd18002
DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 ...
 9-90 6.22e-19

DEAQ-box helicase domain of INO80; INO80 is the catalytic ATPase subunit of the INO80 chromatin remodeling complex. INO80 removes histone H3-containing nucleosomes from associated chromatin, promotes CENP-ACnp1 chromatin assembly at the centromere in a redundant manner with another chromatin-remodeling factor Chd1Hrp1. INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. INO80 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350760 [Multi-domain]  Cd Length: 229  Bit Score: 85.63  E-value: 6.22e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   9 LKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWF--DITSLSETAEDIiakerEQNVLHMLHQILTPF 86
Cdd:cd18002  151 LLSFHCRNRLLLTGTPIQNSMAELWALLHFIMPTLFDSHDEFNEWFskDIESHAENKTGL-----NEHQLKRLHMILKPF 225


                 ....
gi 569006445  87 LLRR 90
Cdd:cd18002  226 MLRR 229
DEXHc_CHD1_2 cd17993
DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and ...
 5-90 1.23e-18

DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and similar proteins; Chromodomain-helicase-DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin-remodeling factor which functions as the substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. It is not only involved in transcription-related chromatin-remodeling, but is also required to maintain a specific chromatin configuration across the genome. CHD1 is also associated with histone deacetylase (HDAC) activity. Chromodomain-helicase-DNA-binding protein 2 (CHD2) is a DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. It is involved in myogenesis via interaction with MYOD1; it binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression. Both are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350751 [Multi-domain]  Cd Length: 218  Bit Score: 84.33  E-value: 1.23e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   5 LIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFEswfdiTSLSETAEDIIAKereqnvlhmLHQILT 84
Cdd:cd17993  147 LYEALKEFKTNNRLLITGTPLQNSLKELWALLHFLMPGKFDIWEEFE-----EEHDEEQEKGIAD---------LHKELE 212


                 ....*.
gi 569006445  85 PFLLRR 90
Cdd:cd17993  213 PFILRR 218
DEXHc_CHD6_7_8_9 cd17995
DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; ...
 3-90 3.14e-18

DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9; Chromodomain-helicase-DNA-binding protein 6-9 (CHD6, CHD7, CHD8, and CHD9) are members of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350753 [Multi-domain]  Cd Length: 223  Bit Score: 83.45  E-value: 3.14e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   3 CRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWF-DItslsETAEDIiakEReqnvlhmLHQ 81
Cdd:cd17995  149 SKLLQGLKKLTLEHKLLLTGTPLQNNTEELWSLLNFLEPEKFPSSEEFLEEFgDL----KTAEQV---EK-------LQA 214


                 ....*....
gi 569006445  82 ILTPFLLRR 90
Cdd:cd17995  215 LLKPYMLRR 223
DEXQc_arch_SWI2_SNF2 cd18012
DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging ...
 9-92 5.15e-18

DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins; Proteins belonging to SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprises a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. Archaeal SWI2 and SNF2 are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350770 [Multi-domain]  Cd Length: 218  Bit Score: 82.61  E-value: 5.15e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   9 LKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDITslsetaediIAKEREQNVLHMLHQILTPFLL 88
Cdd:cd18012  144 VKALKADHRLALTGTPIENHLGELWSIFDFLNPGLLGSYKRFKKRFAKP---------IEKDGDEEALEELKKLISPFIL 214


                 ....
gi 569006445  89 RRLK 92
Cdd:cd18012  215 RRLK 218
DEXHc_CHD2 cd18054
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; ...
 5-90 5.82e-18

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2; Chromodomain-helicase-DNA-binding protein 2 (CHD2) is a DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. It is involved in myogenesis via interaction with MYOD1; it binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression. CHD2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350812 [Multi-domain]  Cd Length: 237  Bit Score: 83.13  E-value: 5.82e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   5 LIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDvfddlkSFESWFDItslsetaEDIIAKEREqNVLHMLHQILT 84
Cdd:cd18054  166 LYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPE------KFEFWEDF-------EEDHGKGRE-NGYQSLHKVLE 231


                 ....*.
gi 569006445  85 PFLLRR 90
Cdd:cd18054  232 PFLLRR 237
DEXHc_SMARCA4 cd18062
DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent ...
 3-92 6.49e-18

DEXH-box helicase domain of SMARCA4; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 (SMARCA4, also known as transcription activator BRG1) is a component of the CREST-BRG1 complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders. SMARCA4 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350820 [Multi-domain]  Cd Length: 251  Bit Score: 83.17  E-value: 6.49e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   3 CRLIRELK-RFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDiTSLSETAEDIIAKEREQN-VLHMLH 80
Cdd:cd18062  161 CKLTQVLNtHYVAPRRLLLTGTPLQNKLPELWALLNFLLPTIFKSCSTFEQWFN-APFAMTGEKVDLNEEETIlIIRRLH 239

                         90
                 ....*....|..
gi 569006445  81 QILTPFLLRRLK 92
Cdd:cd18062  240 KVLRPFLLRRLK 251
DEXHc_SMARCA2 cd18063
DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent ...
 3-92 8.22e-18

DEXH-box helicase domain of SMARCA2; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 (SMARCA2, also known as brahma homolog) is a component of the BAF complex. SMARCA2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350821 [Multi-domain]  Cd Length: 251  Bit Score: 82.80  E-value: 8.22e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   3 CRLIRELK-RFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDiTSLSETAEDIIAKEREQN-VLHMLH 80
Cdd:cd18063  161 CKLTQVLNtHYVAPRRILLTGTPLQNKLPELWALLNFLLPTIFKSCSTFEQWFN-APFAMTGERVDLNEEETIlIIRRLH 239

                         90
                 ....*....|..
gi 569006445  81 QILTPFLLRRLK 92
Cdd:cd18063  240 KVLRPFLLRRLK 251
DEXHc_CHD3_4_5 cd17994
DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; ...
 7-90 1.75e-16

DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5; Chromodomain-helicase-DNA-binding protein 3 (CHD3) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. It is required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity. Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. It is thought to specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3 and plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. As a tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. CHD3, CHD4, and CHD5 are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350752 [Multi-domain]  Cd Length: 196  Bit Score: 77.86  E-value: 1.75e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   7 RELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDITSlsetAEDIIAKereqnvlhmLHQILTPF 86
Cdd:cd17994  126 RILNSYKIGYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLQGFLEEFADIS----KEDQIKK---------LHDLLGPH 192


                 ....
gi 569006445  87 LLRR 90
Cdd:cd17994  193 MLRR 196
DEXHc_Mot1 cd17999
DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in ...
 2-90 6.81e-16

DEXH-box helicase domain of Mot1; Modifier of transcription 1 (Mot1, also known as TAF172 in eukaryotes) regulates transcription in association with TATA binding protein (TBP). Mot1, Ino80C, and NC2 function coordinately to regulate pervasive transcription in yeast and mammals. Mot1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350757 [Multi-domain]  Cd Length: 232  Bit Score: 77.01  E-value: 6.81e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   2 KCRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFD---ITSLSETAEdiiAKEREQNVLHM 78
Cdd:cd17999  142 KTKLSKAVKQLKANHRLILSGTPIQNNVLELWSLFDFLMPGYLGTEKQFQRRFLkpiLASRDSKAS---AKEQEAGALAL 218

                         90
                 ....*....|....
gi 569006445  79 --LHQILTPFLLRR 90
Cdd:cd17999  219 eaLHKQVLPFLLRR 232
DEXHc_Snf cd17919
DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting ...
 2-44 1.52e-14

DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins; Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350677 [Multi-domain]  Cd Length: 182  Bit Score: 71.83  E-value: 1.52e-14
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 569006445   2 KCRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVF 44
Cdd:cd17919  137 KSQLSKALKALRAKRRLLLTGTPLQNNLEELWALLDFLDPPFL 179
DEXHc_CHD1L cd18006
DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, ...
 9-90 1.74e-13

DEAH/Q-box helicase domain of CHD1L; Chromodomain helicase DNA binding protein 1 like (CHD1L, also known as ALC1) is involved in DNA repair by regulating chromatin relaxation following DNA damage. CHD1L is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350764 [Multi-domain]  Cd Length: 216  Bit Score: 69.39  E-value: 1.74e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   9 LKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVF--DDLKSFESWF-DITSLSETAEDiiakereqnvlhmLHQILTP 85
Cdd:cd18006  145 LSEFSVDFRLLLTGTPIQNSLQELYALLSFIEPNVFpkDKLDDFIKAYsETDDESETVEE-------------LHLLLQP 211


                 ....*
gi 569006445  86 FLLRR 90
Cdd:cd18006  212 FLLRR 216
DEXHc_CHD3 cd18055
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; ...
 2-90 6.92e-13

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3; Chromodomain-helicase-DNA-binding protein 3 (CHD3) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. It is required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity. CHD3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350813 [Multi-domain]  Cd Length: 232  Bit Score: 68.11  E-value: 6.92e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   2 KCRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSF-ESWFDITSlsetaEDIIAKereqnvlhmLH 80
Cdd:cd18055  157 QSKFFRVLNGYKIDHKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFlEEFADISK-----EDQIKK---------LH 222

                         90
                 ....*....|
gi 569006445  81 QILTPFLLRR 90
Cdd:cd18055  223 DLLGPHMLRR 232
DEXHc_ERCC6L cd18001
DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint ...
 2-90 1.36e-12

DEXH-box helicase domain of ERCC6L; ERCC excision repair 6 like, spindle assembly checkpoint helicase (ERCC6L, also known as RAD26L) is an essential component of the mitotic spindle assembly checkpoint, by acting as a tension sensor that associates with catenated DNA which is stretched under tension until it is resolved during anaphase. ERCC6L is proposed to stimulate cancer cell proliferation by promoting cell cycle through a way of RAB31-MAPK-CDK2. ERCC6L is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350759 [Multi-domain]  Cd Length: 232  Bit Score: 67.01  E-value: 1.36e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   2 KCRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLP-DVFDDLKSFESWFDITSLSETAEDIIAKERE--QNVLHM 78
Cdd:cd18001  141 KTKSAKSLREIPAKNRIILTGTPIQNNLKELWALFDFACNgSLLGTRKTFKMEFENPITRGRDKDATQGEKAlgSEVAEN 220

                         90
                 ....*....|..
gi 569006445  79 LHQILTPFLLRR 90
Cdd:cd18001  221 LRQIIKPYFLRR 232
DEXHc_RAD54 cd18004
DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are ...
 1-90 1.52e-12

DEXH-box helicase domain of RAD54; RAD54 proteins play a role in recombination. They are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350762 [Multi-domain]  Cd Length: 240  Bit Score: 67.31  E-value: 1.52e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   1 MKCRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFD--ITSLSETAEDIIAKEREQNVLHM 78
Cdd:cd18004  149 SESKTTKALNSLPCRRRLLLTGTPIQNDLDEFFALVDFVNPGILGSLASFRKVFEepILRSRDPDASEEDKELGAERSQE 228

                         90
                 ....*....|..
gi 569006445  79 LHQILTPFLLRR 90
Cdd:cd18004  229 LSELTSRFILRR 240
DEXHc_CHD5 cd18057
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; ...
 2-90 2.87e-12

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5; Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. It is thought to specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3 and plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. As a tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. CHD5 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350815 [Multi-domain]  Cd Length: 232  Bit Score: 66.24  E-value: 2.87e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   2 KCRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSF-ESWFDITSlsetaEDIIAKereqnvlhmLH 80
Cdd:cd18057  157 QSKFFRVLNSYKIDYKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFlEEFADISK-----EDQIKK---------LH 222

                         90
                 ....*....|
gi 569006445  81 QILTPFLLRR 90
Cdd:cd18057  223 DLLGPHMLRR 232
DEXDc_SHPRH-like cd18008
DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the ...
 4-90 1.34e-11

DEXH-box helicase domain of SHPRH-like proteins; The SHPRH-like subgroup belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350766 [Multi-domain]  Cd Length: 241  Bit Score: 64.23  E-value: 1.34e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   4 RLIRELKrfnADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFesWFDITSLSetaediiaKEREQNVLHMLHQIL 83
Cdd:cd18008  168 RAVCALK---AERRWCLTGTPIQNSLDDLYSLLRFLRVEPFGDYPWF--NSDISKPF--------SKNDRKALERLQALL 234


                 ....*..
gi 569006445  84 TPFLLRR 90
Cdd:cd18008  235 KPILLRR 241
DEXHc_CHD4 cd18056
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; ...
 2-90 1.63e-11

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4; Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. CHD4 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350814 [Multi-domain]  Cd Length: 232  Bit Score: 63.93  E-value: 1.63e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   2 KCRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFeswfditsLSETAEdiIAKEREqnvLHMLHQ 81
Cdd:cd18056  157 QSKFFRVLNGYSLQHKLLLTGTPLQNNLEELFHLLNFLTPERFHNLEGF--------LEEFAD--IAKEDQ---IKKLHD 223


                 ....*....
gi 569006445  82 ILTPFLLRR 90
Cdd:cd18056  224 MLGPHMLRR 232
DEXHc_CHD1 cd18053
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; ...
 5-90 6.26e-11

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1; Chromodomain-helicase-DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. It is not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome. CHD1 is also associated with histone deacetylase (HDAC) activity. It is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350811 [Multi-domain]  Cd Length: 237  Bit Score: 62.37  E-value: 6.26e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   5 LIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDvfddlkSFESWfditslsETAEDIIAKEREQNVLHmLHQILT 84
Cdd:cd18053  166 LYKTLIDFKSNHRLLITGTPLQNSLKELWSLLHFIMPE------KFSSW-------EDFEEEHGKGREYGYAS-LHKELE 231


                 ....*.
gi 569006445  85 PFLLRR 90
Cdd:cd18053  232 PFLLRR 237
DEXHc_SMARCAD1 cd17998
DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent ...
 7-44 9.43e-11

DEXH-box helicase domain of SMARCAD1; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (SMARCAD1, also known as ATP-dependent helicase 1 or Hel1) possesses intrinsic ATP-dependent nucleosome-remodeling activity and is required for both DNA repair and heterochromatin organization. SMARCAD1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350756 [Multi-domain]  Cd Length: 187  Bit Score: 60.86  E-value: 9.43e-11
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 569006445   7 RELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVF 44
Cdd:cd17998  146 RHLMTINANFRLLLTGTPLQNNLLELMSLLNFIMPKPF 183
DEXHc_CHD6 cd18058
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; ...
 3-90 3.10e-10

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6; Chromodomain-helicase-DNA-binding protein 6 (CHD6) is a DNA-dependent ATPase that plays a role in chromatin remodeling. It regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin. It activates transcription of specific genes in response to oxidative stress through interaction with NFE2L2.2 and acts as a transcriptional repressor of different viruses including influenza virus or papillomavirus. During influenza virus infection, the viral polymerase complex localizes CHD6 to inactive chromatin where it gets degraded in a proteasome independent-manner. CHD6 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350816 [Multi-domain]  Cd Length: 222  Bit Score: 60.06  E-value: 3.10e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   3 CRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSF-ESWFDItslsetaediiaKEREQnvLHMLHQ 81
Cdd:cd18058  148 CKLLEGLKLMALEHKVLLTGTPLQNSVEELFSLLNFLEPSQFPSETTFlEEFGDL------------KTEEQ--VKKLQS 213


                 ....*....
gi 569006445  82 ILTPFLLRR 90
Cdd:cd18058  214 ILKPMMLRR 222
DISARM_DrmD_b NF038318
DISARM system SNF2-like helicase DrmD, short form; DrmD, a SNF2-like helicase, is a component ...
 17-381 3.71e-10

DISARM system SNF2-like helicase DrmD, short form; DrmD, a SNF2-like helicase, is a component of class 1 DISARM (Defence Island System Associated with Restriction Modification), which contains a DNA adenine N6 methyltransferase. This HMM describes a distinct form that is somewhat shorter than the majority of DrmD proteins.


Pssm-ID: 468472 [Multi-domain]  Cd Length: 868  Bit Score: 62.39  E-value: 3.71e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  17 KLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFdITSlsetaEDIIAKEREqnvlhmlhqiLTPFLLRRLKSDVA 96
Cdd:NF038318 183 KILLTATPLQNSLLDLYGLVSFIDPRIFGSEKVFSKRY-IKD-----EDYSDLKRE----------LSPVLYRTLRKDVA 246

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  97 --------------LEVPPKrEVVVYAPLCN--KQEIFYtAI--VNRT-----IANMFGSCE---KETVELSptgrpKRR 150
Cdd:NF038318 247 dymqfkkrkcitvdFELSPD-EIELYVRVNNflKRDILY-SIptSNRTliilvIRKLLASSSfalAETFEVL-----KKR 319

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445 151 ------SRKSINYSE-LDQFPSELEKLISQ-----------------IQPEVNRERTVVEGNIPIESevNLKLRNIMMLL 206
Cdd:NF038318 320 leklkeGTRSANAQEgFDLFWSFVEDEIDEsgfeekqdelytrqkefIQHEIDEVDAIIDVAKRIKT--NAKVTALKTAL 397

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445 207 RKCCNHpymieypidpvTQEFKIDEELVTNSGKFLILDRMLPELKKRGHK---VLVFSQMTS--MLDILMDYCHLRNF-- 279
Cdd:NF038318 398 EIAFEY-----------QREEGIAQKVVVFTESKRTQKYIAEELRKSGYEgedILLFNGDFDdaMTKEIYRAWQVKNYgk 466

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445 280 -IFSRldgSMSYsereKN--IYSFNTDPDVflfLVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPV 356
Cdd:NF038318 467 aNYGR---SVEY----KHaiVDYFKNNAKI---LIVTDAGSEGLNLQFCNTVINYDLPWNPQKIEQRIGRCHRYGQKNDV 536

                        410       420
                 ....*....|....*....|....*.
gi 569006445 357 VVYRLV-TANTIDQKIVERAAAKRKL 381
Cdd:NF038318 537 VAINLLnTQNVADKRVYEILSEKFEL 562
DEXHc_CHD7 cd18059
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; ...
 3-90 4.68e-10

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7; Chromodomain-helicase-DNA-binding protein 7 (CHD7) is a probable transcription regulator. It may be involved in the 45S precursor rRNA production. CHD7 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350817 [Multi-domain]  Cd Length: 222  Bit Score: 59.66  E-value: 4.68e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   3 CRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDitslsetaeDIIAKEREQNvlhmLHQI 82
Cdd:cd18059  148 CKLLEGLKMMDLEHKVLLTGTPLQNTVEELFSLLHFLEPSRFPSETTFMQEFG---------DLKTEEQVQK----LQAI 214


                 ....*...
gi 569006445  83 LTPFLLRR 90
Cdd:cd18059  215 LKPMMLRR 222
DEXHc_CHD8 cd18060
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; ...
 3-90 3.26e-09

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8; Chromodomain-helicase-DNA-binding protein 8 (CHD8) is a DNA helicase that acts as a chromatin remodeling factor and regulates transcription. It also acts as a transcription repressor by remodeling chromatin structure and recruiting histone H1 to target genes. It suppresses p53/TP53-mediated apoptosis by recruiting histone H1 and preventing p53/TP53 transactivation activity and of STAT3 activity by suppressing the LIF-induced STAT3 transcriptional activity. It also acts as a negative regulator of Wnt signaling pathway and CTNNB1-targeted gene expression. CHD8 is also involved in both enhancer blocking and epigenetic remodeling at chromatin boundary via its interaction with CTCF. It also acts as a transcription activator via its interaction with ZNF143 by participating in efficient U6 RNA polymerase III transcription. CHD8 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350818 [Multi-domain]  Cd Length: 222  Bit Score: 56.99  E-value: 3.26e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   3 CRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDitslsetaeDIIAKEREQNvlhmLHQI 82
Cdd:cd18060  148 CKLLDSLKHMDLEHKVLLTGTPLQNTVEELFSLLHFLEPSQFPSESEFLKDFG---------DLKTEEQVQK----LQAI 214


                 ....*...
gi 569006445  83 LTPFLLRR 90
Cdd:cd18060  215 LKPMMLRR 222
DEXHc_ERCC6 cd18000
DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, ...
 7-41 8.39e-09

DEXH-box helicase domain of ERCC6; ERCC excision repair 6, chromatin remodeling factor (ERCC6, also known Cockayne syndrome group B (CSB), Rad26 in Saccharomyces cerevisiae, and Rhp26 in Schizosaccharomyces pombe) is a DNA-binding protein that is important in transcription-coupled excision repair. ERCC6 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350758 [Multi-domain]  Cd Length: 193  Bit Score: 55.41  E-value: 8.39e-09
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 569006445   7 RELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLP 41
Cdd:cd18000  153 LACKQLRTPHRLILSGTPIQNNLKELWSLFDFVFP 187
DEXHc_CHD9 cd18061
DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; ...
 3-90 1.45e-08

DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9; Chromodomain-helicase-DNA-binding protein 9 (CHD9) acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors. It is proposed to be a ATP-dependent chromatin remodeling protein. CHD9 has DNA-dependent ATPase activity and binds to A/T-rich DNA. It also associates with A/T-rich regulatory regions in promoters of genes that participate in the differentiation of progenitors during osteogenesis. CHD9 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350819 [Multi-domain]  Cd Length: 222  Bit Score: 55.01  E-value: 1.45e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   3 CRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDitslsetaeDIIAKEREQNvlhmLHQI 82
Cdd:cd18061  148 CKLLEGLKLMNLEHKVLLTGTPLQNTVEELFSLLHFLEPLRFPSESTFMQEFG---------DLKTEEQVQK----LQAI 214


                 ....*...
gi 569006445  83 LTPFLLRR 90
Cdd:cd18061  215 LKPMMLRR 222
DEXHc_ERCC6L2 cd18005
DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as ...
 2-90 6.46e-08

DEXH-box helicase domain of ERCC6L2; ERCC excision repair 6 like 2 (ERCC6L2, also known as RAD26L) may play a role in DNA repair and mitochondrial function. In humans, mutations in the ERCC6L2 gene are associated with bone marrow failure syndrome 2. ERCC6L2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350763 [Multi-domain]  Cd Length: 245  Bit Score: 53.54  E-value: 6.46e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   2 KCRLIRELKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDI-----TSLSETAEDI-IAKEREQnv 75
Cdd:cd18005  155 KSKLTQAMKELKCKVRIGLTGTLLQNNMKELWCLLDWAVPGALGSRSQFKKHFSEpikrgQRHTATARELrLGRKRKQ-- 232

                         90
                 ....*....|....*
gi 569006445  76 lhMLHQILTPFLLRR 90
Cdd:cd18005  233 --ELAVKLSKFFLRR 245
DEXHc_ATRX-like cd18007
DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as ...
 9-54 7.70e-08

DEXH-box helicase domain of ATRX-like proteins; This family includes ATRX-like members such as transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) which is involved in transcriptional regulation and chromatin remodeling, and ARIP4 (also called androgen receptor-interacting protein 4, RAD54 like 2 or RAD54L2) which modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. They are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350765 [Multi-domain]  Cd Length: 239  Bit Score: 53.06  E-value: 7.70e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 569006445   9 LKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWF 54
Cdd:cd18007  171 LSKVKTKRRILLTGTPLQNNLKEYWTMVDFARPKYLGTLKEFKKKF 216
DEXHc_RAD54A cd18067
DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as ...
 9-90 6.23e-07

DEXH-box helicase domain of RAD54A; DNA repair and recombination protein RAD54A, also known as RAD54L or RAD54, plays a role in homologous recombination related repair of DNA double-strand breaks. RAD54A is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350825 [Multi-domain]  Cd Length: 243  Bit Score: 50.55  E-value: 6.23e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   9 LKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDITSLSETAEDIIAKEREQNV--LHMLHQILTPF 86
Cdd:cd18067  160 LDSLNTQRRVLLSGTPIQNDLSEYFSLVNFVNPGILGTAAEFKKNFELPILKGRDADASEKERQLGEekLQELISIVNRC 239


                 ....
gi 569006445  87 LLRR 90
Cdd:cd18067  240 IIRR 243
DEXHc_TTF2 cd18072
DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called ...
 20-90 7.64e-07

DEAH-box helicase domain of TTF2; Transcription termination factor 2 (TTF2 also called Forkhead-box E1/FOXE1 ) is a transcription termination factor that couples ATP hydrolysis with the removal of RNA polymerase II from the DNA template. Single nucleotide polymorphism (SNP) within the 5'-UTR of TTF2 is associated with thyroid cancer risk.TTF2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350830 [Multi-domain]  Cd Length: 241  Bit Score: 50.17  E-value: 7.64e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 569006445  20 LTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFDITSLSetaediiAKEReqnvlhmLHQILTPFLLRR 90
Cdd:cd18072  185 LTGTPIQNNLLDMYSLLKFLRCSPFDDLKVWKKQVDNKSRK-------GGER-------LNILTKSLLLRR 241
SSL2 COG1061
Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];
214-451 1.87e-06

Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair];


Pssm-ID: 440681 [Multi-domain]  Cd Length: 566  Bit Score: 50.41  E-value: 1.87e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445 214 YMIEYPIDPVTQEFKIDEELVT------NSGKFLILDRMLPELKKrGHKVLVFSQMTSMLDILMDYCHLRNFIFSRLDGS 287
Cdd:COG1061  260 YGIRVDLTDERAEYDALSERLRealaadAERKDKILRELLREHPD-DRKTLVFCSSVDHAEALAELLNEAGIRAAVVTGD 338

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445 288 MSYSEREKNIYSFNTDPDVflFLVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPVVVYRLVTANTI 367
Cdd:COG1061  339 TPKKEREEILEAFRDGELR--ILVTVDVLNEGVDVPRLDVAILLRPTGSPREFIQRLGRGLRPAPGKEDALVYDFVGNDV 416

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445 368 DqkIVERAAAKRKLEKLIIHKNHFKGGQSGLSQSKNFLDAKELMELLKSRDYEREVKGSREKVISDEDLELLLDRSDLID 447
Cdd:COG1061  417 P--VLEELAKDLRDLAGYRVEFLDEEESEELALLIAVKPALEVKGELEEELLEELELLEDALLLVLAELLLLELLALALE 494


                 ....
gi 569006445 448 QMKA 451
Cdd:COG1061  495 LLEL 498
SF2_C cd18785
C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases ...
 305-359 5.84e-06

C-terminal helicase domain of superfamily 2 DEAD/H-box helicases; Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350172 [Multi-domain]  Cd Length: 77  Bit Score: 44.23  E-value: 5.84e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 569006445 305 DVFLFLVSTRAGGLGINLTAADTVIIYDSDWNPQSDLQAQDRCHRIGQTKPVVVY 359
Cdd:cd18785   21 SSLEILVATNVLGEGIDVPSLDTVIFFDPPSSAASYIQRVGRAGRGGKDEGEVIL 75
HDA2-3 pfam11496
Class II histone deacetylase complex subunits 2 and 3; This family of class II histone ...
 204-369 6.13e-06

Class II histone deacetylase complex subunits 2 and 3; This family of class II histone deacetylase complex subunits HDA2 and HDA3 is found in fungi, The member from S. pombe is referred to as Ccq1 in Swiss:Q10432. These proteins associate with HDA1 to generate the activity of the HDA1 histone deacetylase complex. HDA1 interacts with itself and with the HDA2-HDA3 subcomplex to form a probable tetramer and these interactions are necessary for catalytic activity. The HDA1 histone deacetylase complex is responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. HDA2 and HDA3 have a conserved coiled-coil domain towards their C-terminus.


Pssm-ID: 402894  Cd Length: 281  Bit Score: 47.71  E-value: 6.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  204 MLLRKCC---NHPYMIEYPIDPVTQEFK-IDEELVTNSGKFLILDRMLPEL----KKRGHKVLVFSQMTSMLDILMDYCH 275
Cdd:pfam11496  52 LCLENLSlvaTHPYLLVDHYMPKSLLLKdEPEKLAYTSGKFLVLNDLVNLLierdRKEPINVAIVARSGKTLDLVEALLL 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445  276 LRNFIFSRLDGSMSYSEREKNIYSFNTDP--DVFLFLVSTR-----AGGLGInlTAADTVIIYDSDWNPQSDLQAQDRCH 348
Cdd:pfam11496 132 GKGLSYKRYSGEMLYGENKKVSDSGNKKIhsTTCHLLSSTGqltndDSLLEN--YKFDLIIAFDSSVDTSSPSVEHLRTQ 209

                         170       180
                  ....*....|....*....|.
gi 569006445  349 RIGQTKPVVVYRLVTANTIDQ 369
Cdd:pfam11496 210 NRRKGNLAPIIRLVVINSIEH 230
DEXDc_RapA cd18011
DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated ...
 4-52 6.76e-06

DEXH-box helicase domain of RapA; In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350769 [Multi-domain]  Cd Length: 207  Bit Score: 46.90  E-value: 6.76e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 569006445   4 RLIRELKRfNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFES 52
Cdd:cd18011  145 KLGRLLAK-RARHVLLLTATPHNGKEEDFRALLSLLDPGRFAVLGRFLR 192
SF2_C_DEAD cd18787
C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse ...
 223-353 2.22e-05

C-terminal helicase domain of the DEAD box helicases; DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC.


Pssm-ID: 350174 [Multi-domain]  Cd Length: 131  Bit Score: 44.04  E-value: 2.22e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445 223 VTQEFkideELVTNSGKFLILDRMLPELKKRGhKVLVFSQMTSMLDILMDYCHLRNFIFSRLDGSMSYSEREKNIYSFNT 302
Cdd:cd18787    1 IKQLY----VVVEEEEKKLLLLLLLLEKLKPG-KAIIFVNTKKRVDRLAELLEELGIKVAALHGDLSQEERERALKKFRS 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 569006445 303 -DPDVflfLVST----RagglGINLTAADTVIIYDsdwNPQSdlqAQDRCHRIGQT 353
Cdd:cd18787   76 gKVRV---LVATdvaaR----GLDIPGVDHVINYD---LPRD---AEDYVHRIGRT 118
DEXHc_ARIP4 cd18069
DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called ...
 9-55 7.87e-05

DEXH-box helicase domain of ARIP4; Androgen receptor-interacting protein 4 (ARIP4, also called RAD54 like 2 or RAD54L2 ) modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. ARIP4 is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350827 [Multi-domain]  Cd Length: 227  Bit Score: 44.04  E-value: 7.87e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 569006445   9 LKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFD 55
Cdd:cd18069  159 LKNIRSRRRIVLTGYPLQNNLIEYWCMVDFVRPDFLGTRQEFSNMFE 205
DEXHc_ATRX cd18068
DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha ...
 17-54 1.24e-03

DEXH-box helicase domain of ATRX; Transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) is involved in transcriptional regulation and chromatin remodeling. Mutations in humans cause mental retardation, X-linked, syndromic, with hypotonic facies 1 (MRXSHF1) and alpha-thalassemia myelodysplasia syndrome (ATMDS). ATRX is part of the a DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350826 [Multi-domain]  Cd Length: 246  Bit Score: 40.64  E-value: 1.24e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 569006445  17 KLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWF 54
Cdd:cd18068  186 RIVLTGTPLQNNLIEYHCMVNFVKPNLLGTIKEFRNRF 223
DEXHc_RAD54B cd18066
DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as ...
 9-90 7.37e-03

DEXH-box helicase domain of RAD54B; DNA repair and recombination protein RAD54B, also known as RDH54, binds to double-stranded DNA, displays ATPase activity in the presence of DNA, and may have a role in meiotic and mitotic recombination. RAD54B is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.


Pssm-ID: 350824 [Multi-domain]  Cd Length: 235  Bit Score: 37.90  E-value: 7.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 569006445   9 LKRFNADNKLLLTGTPLQNNLSELWSLLNFLLPDVFDDLKSFESWFD---ITSLSETA---EDIIAKEREQNvlhmLHQI 82
Cdd:cd18066  152 LTSLSCERRIILTGTPIQNDLQEFFALIDFVNPGILGSLSTYRKVYEepiVRSREPTAtpeEKKLGEARAAE----LTRL 227


                 ....*...
gi 569006445  83 LTPFLLRR 90
Cdd:cd18066  228 TGLFILRR 235
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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